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<h1 class="epydoc">Source Code for <a href="trunk.BIP.Bayes.general.bvariables-module.html">Module trunk.BIP.Bayes.general.bvariables</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-docstring">This module implements classes to represent an arbitrary Bayesian random variable.</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-docstring">This is experimental code! do not use for serious applications!</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-comment"># copyright 2007 Flavio Codeco Coelho</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt class="py-comment"># Licensed under GPL v3</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package trunk.BIP=trunk.BIP-module.html"><a title="trunk.BIP" class="py-name" href="#" onclick="return doclink('link-0', 'BIP', 'link-0');">BIP</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package trunk.BIP.Bayes=trunk.BIP.Bayes-module.html"><a title="trunk.BIP.Bayes" class="py-name" href="#" onclick="return doclink('link-1', 'Bayes', 'link-1');">Bayes</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Module trunk.BIP.Bayes.like=trunk.BIP.Bayes.like-module.html"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-2', 'like', 'link-2');">like</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">arange</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">array</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">compress</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">exp</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">greater</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">less</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">ones</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">searchsorted</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">sqrt</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">pylab</tt> <tt class="py-keyword">as</tt> <tt class="py-name">P</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">scipy</tt> <tt class="py-keyword">import</tt> <tt class="py-name">stats</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="trunk.BIP" class="py-name" href="#" onclick="return doclink('link-3', 'BIP', 'link-0');">BIP</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Variable trunk.BIP.Bayes.Melding.Viz=trunk.BIP.Bayes.Melding-module.html#Viz,Package trunk.BIP.Viz=trunk.BIP.Viz-module.html"><a title="trunk.BIP.Bayes.Melding.Viz
trunk.BIP.Viz" class="py-name" href="#" onclick="return doclink('link-4', 'Viz', 'link-4');">Viz</a></tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Module trunk.BIP.Viz.asciihist=trunk.BIP.Viz.asciihist-module.html"><a title="trunk.BIP.Viz.asciihist" class="py-name" href="#" onclick="return doclink('link-5', 'asciihist', 'link-5');">asciihist</a></tt> <tt class="py-keyword">import</tt> <tt id="link-6" class="py-name" targets="Class trunk.BIP.Viz.ascii.Histogram=trunk.BIP.Viz.ascii.Histogram-class.html,Class trunk.BIP.Viz.asciihist.Histogram=trunk.BIP.Viz.asciihist.Histogram-class.html"><a title="trunk.BIP.Viz.ascii.Histogram
trunk.BIP.Viz.asciihist.Histogram" class="py-name" href="#" onclick="return doclink('link-6', 'Histogram', 'link-6');">Histogram</a></tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line"><tt class="py-comment">## Conjugate prior list: distribution types which have supported conjugate prior </tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line"><tt id="link-7" class="py-name" targets="Variable trunk.BIP.Bayes.general.bvariables.discrete_conjugate_priors=trunk.BIP.Bayes.general.bvariables-module.html#discrete_conjugate_priors"><a title="trunk.BIP.Bayes.general.bvariables.discrete_conjugate_priors" class="py-name" href="#" onclick="return doclink('link-7', 'discrete_conjugate_priors', 'link-7');">discrete_conjugate_priors</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-string">'Bernoulli'</tt><tt class="py-op">:</tt><tt class="py-string">'Beta'</tt><tt class="py-op">,</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-string">'Binomial'</tt><tt class="py-op">:</tt><tt class="py-string">'Beta'</tt><tt class="py-op">,</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-string">'Negative Binomial'</tt><tt class="py-op">:</tt><tt class="py-string">'Beta'</tt><tt class="py-op">,</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">    <tt class="py-string">'Poisson'</tt><tt class="py-op">:</tt><tt class="py-string">'Gamma'</tt><tt class="py-op">,</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">    <tt class="py-string">'Multinomial'</tt><tt class="py-op">:</tt><tt class="py-string">'Dirichlet'</tt><tt class="py-op">,</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">    <tt class="py-string">'Geometric'</tt><tt class="py-op">:</tt><tt class="py-string">'Beta'</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-op">}</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line"><tt id="link-8" class="py-name" targets="Variable trunk.BIP.Bayes.general.bvariables.continuous_conjugate_priors=trunk.BIP.Bayes.general.bvariables-module.html#continuous_conjugate_priors"><a title="trunk.BIP.Bayes.general.bvariables.continuous_conjugate_priors" class="py-name" href="#" onclick="return doclink('link-8', 'continuous_conjugate_priors', 'link-8');">continuous_conjugate_priors</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">    <tt class="py-string">'Uniform'</tt><tt class="py-op">:</tt><tt class="py-string">'Pareto'</tt><tt class="py-op">,</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">    <tt class="py-string">'Exponential'</tt><tt class="py-op">:</tt><tt class="py-string">'Gamma'</tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">    <tt class="py-string">'Normal'</tt><tt class="py-op">:</tt><tt class="py-string">'Normal'</tt><tt class="py-op">,</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">    <tt class="py-string">'Pareto'</tt><tt class="py-op">:</tt><tt class="py-string">'Gamma'</tt><tt class="py-op">,</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">    <tt class="py-string">'Gamma'</tt><tt class="py-op">:</tt><tt class="py-string">'Gamma'</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">    <tt class="py-string">'Inverse Gamma'</tt><tt class="py-op">:</tt><tt class="py-string">'Gamma'</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">    <tt class="py-op">}</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"> </tt>
<a name="BayesVar"></a><div id="BayesVar-def"><a name="L45"></a><tt class="py-lineno"> 45</tt> <a class="py-toggle" href="#" id="BayesVar-toggle" onclick="return toggle('BayesVar');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables-module.html#BayesVar">BayesVar</a><tt class="py-op">(</tt><tt class="py-param">priortype</tt><tt class="py-op">,</tt> <tt class="py-param">pars</tt><tt class="py-op">,</tt> <tt class="py-param">range</tt><tt class="py-op">,</tt> <tt class="py-param">resolution</tt><tt class="py-op">=</tt><tt class="py-number">1024</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="BayesVar-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="BayesVar-expanded"><a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">    Factory function for continuous and discrete variables</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">priortype</tt><tt class="py-op">,</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">rv_continuous</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-9" class="py-name" targets="Class trunk.BIP.Bayes.general.bvariables.__BayesC=trunk.BIP.Bayes.general.bvariables.__BayesC-class.html"><a title="trunk.BIP.Bayes.general.bvariables.__BayesC" class="py-name" href="#" onclick="return doclink('link-9', '__BayesC', 'link-9');">__BayesC</a></tt><tt class="py-op">(</tt><tt class="py-name">priortype</tt><tt class="py-op">,</tt> <tt class="py-name">pars</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">,</tt> <tt class="py-name">resolution</tt><tt class="py-op">)</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">disttype</tt><tt class="py-op">,</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">rv_discrete</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt id="link-10" class="py-name" targets="Class trunk.BIP.Bayes.general.bvariables.__BayesD=trunk.BIP.Bayes.general.bvariables.__BayesD-class.html"><a title="trunk.BIP.Bayes.general.bvariables.__BayesD" class="py-name" href="#" onclick="return doclink('link-10', '__BayesD', 'link-10');">__BayesD</a></tt><tt class="py-op">(</tt><tt class="py-name">priortype</tt><tt class="py-op">,</tt> <tt class="py-name">pars</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">,</tt> <tt class="py-name">resolution</tt><tt class="py-op">)</tt> </tt>
</div><a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"> </tt>
<a name="_BayesVar"></a><div id="_BayesVar-def"><a name="L55"></a><tt class="py-lineno"> 55</tt> <a class="py-toggle" href="#" id="_BayesVar-toggle" onclick="return toggle('_BayesVar');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html">_BayesVar</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_BayesVar-expanded"><a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-docstring">    Bayesian random variate.</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="_BayesVar.__init__"></a><div id="_BayesVar.__init__-def"><a name="L59"></a><tt class="py-lineno"> 59</tt> <a class="py-toggle" href="#" id="_BayesVar.__init__-toggle" onclick="return toggle('_BayesVar.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">disttype</tt><tt class="py-op">,</tt> <tt class="py-param">pars</tt><tt class="py-op">,</tt> <tt class="py-param">rang</tt><tt class="py-op">,</tt> <tt class="py-param">resolution</tt><tt class="py-op">=</tt><tt class="py-number">1024</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar.__init__-expanded"><a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-docstring">        Initializes random variable.</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-docstring">        :parameters:</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line"><tt class="py-docstring">            - `disttype`: must be a valid RNG class from scipy.stats</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line"><tt class="py-docstring">            - `pars`: are the parameters of the distribution.</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line"><tt class="py-docstring">            - `rang`: range of the variable support.</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line"><tt class="py-docstring">            - `resolution`: resolution of the support.</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">distn</tt> <tt class="py-op">=</tt> <tt class="py-name">disttype</tt><tt class="py-op">.</tt><tt class="py-name">name</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Method trunk.BIP.Bayes.general.bvariables._BayesVar._flavorize()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#_flavorize"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar._flavorize" class="py-name" href="#" onclick="return doclink('link-11', '_flavorize', 'link-11');">_flavorize</a></tt><tt class="py-op">(</tt><tt class="py-name">disttype</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt class="py-name">pars</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">disttype</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pars</tt> <tt class="py-op">=</tt> <tt class="py-name">pars</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt> <tt class="py-op">=</tt> <tt class="py-name">rang</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-number">1.</tt> <tt class="py-op">/</tt> <tt class="py-name">resolution</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likelihood</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">posterior</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line"> </tt>
<a name="_BayesVar.__str__"></a><div id="_BayesVar.__str__-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="_BayesVar.__str__-toggle" onclick="return toggle('_BayesVar.__str__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#__str__">__str__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar.__str__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar.__str__-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line"><tt class="py-docstring">        :Return:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line"><tt class="py-docstring">            ascii histogram of the variable</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">posterior</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">            <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">posterior</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">            <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-12" class="py-name" targets="Method trunk.BIP.Bayes.general.bvariables._BayesVar.get_posterior_sample()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#get_posterior_sample"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar.get_posterior_sample" class="py-name" href="#" onclick="return doclink('link-12', 'get_posterior_sample', 'link-12');">get_posterior_sample</a></tt><tt class="py-op">(</tt><tt class="py-number">200000</tt><tt class="py-op">)</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">        <tt class="py-name">name</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">distn</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pars</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name" targets="Method trunk.BIP.Bayes.general.bvariables._BayesVar.__str__()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#__str__"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar.__str__" class="py-name" href="#" onclick="return doclink('link-13', '__str__', 'link-13');">__str__</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">        <tt class="py-name">h</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name"><a title="trunk.BIP.Viz.ascii.Histogram
trunk.BIP.Viz.asciihist.Histogram" class="py-name" href="#" onclick="return doclink('link-14', 'Histogram', 'link-6');">Histogram</a></tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt> <tt class="py-name">bins</tt><tt class="py-op">=</tt><tt class="py-number">10</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">name</tt> <tt class="py-op">+</tt> <tt class="py-string">'\n'</tt> <tt class="py-op">+</tt> <tt class="py-name">h</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name" targets="Method trunk.BIP.Viz.ascii.Histogram.vertical()=trunk.BIP.Viz.ascii.Histogram-class.html#vertical,Method trunk.BIP.Viz.asciihist.Histogram.vertical()=trunk.BIP.Viz.asciihist.Histogram-class.html#vertical"><a title="trunk.BIP.Viz.ascii.Histogram.vertical
trunk.BIP.Viz.asciihist.Histogram.vertical" class="py-name" href="#" onclick="return doclink('link-15', 'vertical', 'link-15');">vertical</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"> </tt>
<a name="_BayesVar._flavorize"></a><div id="_BayesVar._flavorize-def"><a name="L92"></a><tt class="py-lineno"> 92</tt> <a class="py-toggle" href="#" id="_BayesVar._flavorize-toggle" onclick="return toggle('_BayesVar._flavorize');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#_flavorize">_flavorize</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">pt</tt><tt class="py-op">,</tt> <tt class="py-param">ptbase</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar._flavorize-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar._flavorize-expanded"><a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line"><tt class="py-docstring">        Add methods from distribution type</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">cdf</tt> <tt class="py-op">=</tt> <tt id="link-16" class="py-name" targets="Variable trunk.BIP.SDE.example.pt=trunk.BIP.SDE.example-module.html#pt"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-16', 'pt', 'link-16');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">cdf</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">isf</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-17', 'pt', 'link-16');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">isf</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">ptbase</tt><tt class="py-op">,</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">rv_continuous</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdf</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-18', 'pt', 'link-16');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">pdf</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">ptbase</tt><tt class="py-op">,</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">rv_discrete</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdf</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-19', 'pt', 'link-16');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">pmf</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">exit</tt><tt class="py-op">(</tt><tt class="py-string">'Invalid distribution object'</tt><tt class="py-op">)</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">ppf</tt> <tt class="py-op">=</tt> <tt id="link-20" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-20', 'pt', 'link-16');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">ppf</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt> <tt class="py-op">=</tt> <tt id="link-21" class="py-name"><a title="trunk.BIP.SDE.example.pt" class="py-name" href="#" onclick="return doclink('link-21', 'pt', 'link-16');">pt</a></tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt> </tt>
</div><a name="_BayesVar._update"></a><div id="_BayesVar._update-def"><a name="L105"></a><tt class="py-lineno">105</tt> <a class="py-toggle" href="#" id="_BayesVar._update-toggle" onclick="return toggle('_BayesVar._update');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#_update">_update</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar._update-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar._update-expanded"><a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-docstring">        Calculate likelihood function</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">!=</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">            <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">            <tt class="py-name">sc</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pars</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">            <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">            <tt id="link-22" class="py-name" targets="Variable trunk.BIP.SDE.example.M=trunk.BIP.SDE.example-module.html#M"><a title="trunk.BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-22', 'M', 'link-22');">M</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">            <tt id="link-23" class="py-name" targets="Method trunk.BIP.Bayes.Samplers.MCMC.Dream.step()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#step,Method trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step()=trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#step"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-23', 'step', 'link-23');">step</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">            <tt class="py-name">likefun</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method trunk.BIP.Bayes.general.bvariables._BayesVar._likelihood()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#_likelihood"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar._likelihood" class="py-name" href="#" onclick="return doclink('link-24', '_likelihood', 'link-24');">_likelihood</a></tt><tt class="py-op">(</tt><tt id="link-25" class="py-name" targets="Function trunk.BIP.Bayes.Melding.model()=trunk.BIP.Bayes.Melding-module.html#model"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-25', 'model', 'link-25');">model</a></tt><tt class="py-op">)</tt><tt class="py-comment">#returns log-likelihood function</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">            <tt class="py-name">lik</tt> <tt class="py-op">=</tt> <tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-name">likefun</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-name">d</tt><tt class="py-op">,</tt> <tt class="py-name">i</tt><tt class="py-op">,</tt> <tt class="py-name">d</tt><tt class="py-op">.</tt><tt class="py-name">var</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">i</tt> <tt class="py-keyword">in</tt> <tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt id="link-26" class="py-name"><a title="trunk.BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-26', 'M', 'link-22');">M</a></tt><tt class="py-op">,</tt> <tt id="link-27" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-27', 'step', 'link-23');">step</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likelihood</tt> <tt class="py-op">=</tt> <tt class="py-name">lik</tt> <tt class="py-op">/</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">lik</tt><tt class="py-op">)</tt> </tt>
</div><a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line"> </tt>
<a name="_BayesVar.add_data"></a><div id="_BayesVar.add_data-def"><a name="L119"></a><tt class="py-lineno">119</tt> <a class="py-toggle" href="#" id="_BayesVar.add_data-toggle" onclick="return toggle('_BayesVar.add_data');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#add_data">add_data</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">,</tt> <tt class="py-param">model</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar.add_data-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar.add_data-expanded"><a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line"><tt class="py-docstring">        Updates variable with information from dataset</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line"><tt class="py-docstring">            - `data`: sequence of numbers</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line"><tt class="py-docstring">            - `model`: probabilistic model underlying data</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">)</tt>  </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name" targets="Method trunk.BIP.Bayes.general.bvariables._BayesVar._update()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#_update"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar._update" class="py-name" href="#" onclick="return doclink('link-28', '_update', 'link-28');">_update</a></tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="trunk.BIP.Bayes.Melding.model" class="py-name" href="#" onclick="return doclink('link-29', 'model', 'link-25');">model</a></tt><tt class="py-op">.</tt><tt class="py-name">dist</tt><tt class="py-op">.</tt><tt class="py-name">name</tt><tt class="py-op">)</tt> </tt>
</div><a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line"> </tt>
<a name="_BayesVar.get_prior_sample"></a><div id="_BayesVar.get_prior_sample-def"><a name="L130"></a><tt class="py-lineno">130</tt> <a class="py-toggle" href="#" id="_BayesVar.get_prior_sample-toggle" onclick="return toggle('_BayesVar.get_prior_sample');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#get_prior_sample">get_prior_sample</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar.get_prior_sample-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar.get_prior_sample-expanded"><a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line"><tt class="py-docstring">        Returns a sample from the prior distribution</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"><tt class="py-docstring">            - `n`: Sample size.</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-name">size</tt><tt class="py-op">=</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
</div><a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">     </tt>
<a name="_BayesVar.get_prior_dist"></a><div id="_BayesVar.get_prior_dist-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="_BayesVar.get_prior_dist-toggle" onclick="return toggle('_BayesVar.get_prior_dist');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#get_prior_dist">get_prior_dist</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar.get_prior_dist-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar.get_prior_dist-expanded"><a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line"><tt class="py-docstring">        Returns the prior PDF.</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdf</tt><tt class="py-op">(</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">         </tt>
<a name="_BayesVar.get_posterior_sample"></a><div id="_BayesVar.get_posterior_sample-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="_BayesVar.get_posterior_sample-toggle" onclick="return toggle('_BayesVar.get_posterior_sample');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#get_posterior_sample">get_posterior_sample</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">n</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar.get_posterior_sample-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar.get_posterior_sample-expanded"><a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line"><tt class="py-docstring">        Return a sample of the posterior distribution.</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line"><tt class="py-docstring">        Uses SIR algorithm.</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line"><tt class="py-docstring">            - `n`: Sample size.</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">posterior</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-comment"># Use last posterior as prior</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">            <tt class="py-name">k</tt> <tt class="py-op">=</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">kde</tt><tt class="py-op">.</tt><tt class="py-name">gaussian_kde</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">posterior</tt><tt class="py-op">)</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">            <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">k</tt><tt class="py-op">.</tt><tt class="py-name">resample</tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">            <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-30" class="py-name" targets="Method trunk.BIP.Bayes.general.bvariables._BayesVar.get_prior_sample()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#get_prior_sample"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar.get_prior_sample" class="py-name" href="#" onclick="return doclink('link-30', 'get_prior_sample', 'link-30');">get_prior_sample</a></tt><tt class="py-op">(</tt><tt class="py-name">n</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt> <tt class="py-op">!=</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">            <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">            <tt id="link-31" class="py-name"><a title="trunk.BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-31', 'M', 'link-22');">M</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">            <tt id="link-32" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-32', 'step', 'link-23');">step</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">res</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">            <tt class="py-name">supp</tt> <tt class="py-op">=</tt> <tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">m</tt><tt class="py-op">,</tt> <tt id="link-33" class="py-name"><a title="trunk.BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-33', 'M', 'link-22');">M</a></tt><tt class="py-op">,</tt> <tt id="link-34" class="py-name"><a title="trunk.BIP.Bayes.Samplers.MCMC.Dream.step
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.step" class="py-name" href="#" onclick="return doclink('link-34', 'step', 'link-23');">step</a></tt><tt class="py-op">)</tt><tt class="py-comment">#support</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">            <tt class="py-name">s</tt> <tt class="py-op">=</tt> <tt class="py-name">compress</tt><tt class="py-op">(</tt><tt class="py-name">less</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name"><a title="trunk.BIP.SDE.example.M" class="py-name" href="#" onclick="return doclink('link-35', 'M', 'link-22');">M</a></tt><tt class="py-op">)</tt> <tt class="py-op">&amp;</tt> <tt class="py-name">greater</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">.</tt><tt class="py-name">ravel</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">m</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-comment">#removing out-of-range samples</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">            <tt class="py-name">d</tt> <tt class="py-op">=</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-name">loc</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-name">scale</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">size</tt><tt class="py-op">=</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">s</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-comment">#Uniform 0-1 samples</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">            <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pdf</tt><tt class="py-op">(</tt><tt class="py-name">supp</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">likelihood</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">            <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">w</tt> <tt class="py-op">/</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">w</tt><tt class="py-op">)</tt> <tt class="py-comment">#normalizing weights</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">            <tt class="py-name">sx</tt> <tt class="py-op">=</tt> <tt class="py-name">searchsorted</tt><tt class="py-op">(</tt><tt class="py-name">supp</tt><tt class="py-op">,</tt> <tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">            <tt class="py-name">w</tt> <tt class="py-op">=</tt> <tt class="py-name">w</tt><tt class="py-op">[</tt><tt class="py-name">sx</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-comment">#search sorted returns 1-based binlist</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line">            <tt class="py-name">post</tt> <tt class="py-op">=</tt> <tt class="py-name">compress</tt><tt class="py-op">(</tt><tt class="py-name">d</tt> <tt class="py-op">&lt;</tt> <tt class="py-name">w</tt><tt class="py-op">,</tt> <tt class="py-name">s</tt><tt class="py-op">)</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line">            <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">posterior</tt> <tt class="py-op">=</tt> <tt class="py-name">post</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">post</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line">        <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> <tt class="py-name">array</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"> </tt>
<a name="_BayesVar._likelihood"></a><div id="_BayesVar._likelihood-def"><a name="L175"></a><tt class="py-lineno">175</tt> <a class="py-toggle" href="#" id="_BayesVar._likelihood-toggle" onclick="return toggle('_BayesVar._likelihood');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#_likelihood">_likelihood</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dname</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar._likelihood-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar._likelihood-expanded"><a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line"><tt class="py-docstring">        Defines parametric family  of the likelihood function.</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line"><tt class="py-docstring">        Returns likelihood function.</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"><tt class="py-docstring">        :Parameters:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"><tt class="py-docstring">            - `dname`: must be a string.</tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line"><tt class="py-docstring">        :Return:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line"><tt class="py-docstring">            lambda function to calculate  the likelihood.</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">        <tt class="py-name">like_funs</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">            <tt class="py-string">'norm'</tt><tt class="py-op">:</tt> <tt class="py-keyword">lambda</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt id="link-36" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-36', 'like', 'link-2');">like</a></tt><tt class="py-op">.</tt><tt id="link-37" class="py-name" targets="Function trunk.BIP.Bayes.like.Normal()=trunk.BIP.Bayes.like-module.html#Normal"><a title="trunk.BIP.Bayes.like.Normal" class="py-name" href="#" onclick="return doclink('link-37', 'Normal', 'link-37');">Normal</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-number">1.</tt> <tt class="py-op">/</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">            <tt class="py-string">'expon'</tt><tt class="py-op">:</tt> <tt class="py-keyword">lambda</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt> <tt class="py-op">/</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">**</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt class="py-name">size</tt> <tt class="py-op">*</tt> <tt class="py-name">exp</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-number">1.</tt> <tt class="py-op">/</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">sum</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">            <tt class="py-string">'beta'</tt><tt class="py-op">:</tt> <tt class="py-keyword">lambda</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt id="link-38" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-38', 'like', 'link-2');">like</a></tt><tt class="py-op">.</tt><tt id="link-39" class="py-name" targets="Function trunk.BIP.Bayes.like.Beta()=trunk.BIP.Bayes.like-module.html#Beta"><a title="trunk.BIP.Bayes.like.Beta" class="py-name" href="#" onclick="return doclink('link-39', 'Beta', 'link-39');">Beta</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">            <tt class="py-string">'uniform'</tt><tt class="py-op">:</tt> <tt class="py-keyword">lambda</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> <tt id="link-40" class="py-name"><a title="trunk.BIP.Bayes.like" class="py-name" href="#" onclick="return doclink('link-40', 'like', 'link-2');">like</a></tt><tt class="py-op">.</tt><tt id="link-41" class="py-name" targets="Function trunk.BIP.Bayes.like.Uniform()=trunk.BIP.Bayes.like-module.html#Uniform"><a title="trunk.BIP.Bayes.like.Uniform" class="py-name" href="#" onclick="return doclink('link-41', 'Uniform', 'link-41');">Uniform</a></tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">-</tt><tt class="py-number">2</tt> <tt class="py-op">*</tt> <tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-number">2</tt> <tt class="py-op">*</tt> <tt class="py-name">sqrt</tt><tt class="py-op">(</tt><tt class="py-name">x</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">        <tt class="py-op">}</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">like_funs</tt><tt class="py-op">[</tt><tt class="py-name">dname</tt><tt class="py-op">]</tt> </tt>
</div><a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">        <tt class="py-comment">#TODO: expand for more distribution types</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">         </tt>
<a name="_BayesVar._post_from_conjugate"></a><div id="_BayesVar._post_from_conjugate-def"><a name="L195"></a><tt class="py-lineno">195</tt> <a class="py-toggle" href="#" id="_BayesVar._post_from_conjugate-toggle" onclick="return toggle('_BayesVar._post_from_conjugate');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#_post_from_conjugate">_post_from_conjugate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">dname</tt><tt class="py-op">,</tt> <tt class="py-op">*</tt> <tt class="py-param">pars</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_BayesVar._post_from_conjugate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="_BayesVar._post_from_conjugate-expanded"><a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">        <tt class="py-docstring">'''</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"><tt class="py-docstring">        Returns posterior distribution function using conjugate prior theory</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line"><tt class="py-docstring">        '''</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">data</tt><tt class="py-op">:</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">            <tt class="py-keyword">return</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">dname</tt> <tt class="py-op">==</tt> <tt class="py-string">'bernoulli'</tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">            <tt class="py-name">pdist</tt> <tt class="py-op">=</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">beta</tt><tt class="py-op">(</tt><tt class="py-name">pars</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">            <tt class="py-comment"># TODO: finish this</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line"> </tt>
<a name="__BayesC"></a><div id="__BayesC-def"><a name="L205"></a><tt class="py-lineno">205</tt> <a class="py-toggle" href="#" id="__BayesC-toggle" onclick="return toggle('__BayesC');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables.__BayesC-class.html">__BayesC</a><tt class="py-op">(</tt><tt class="py-base-class">_BayesVar</tt><tt class="py-op">,</tt> <tt class="py-base-class">stats</tt><tt class="py-op">.</tt><tt class="py-base-class">rv_continuous</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="__BayesC-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__BayesC-expanded"><a name="__BayesC.__init__"></a><div id="__BayesC.__init__-def"><a name="L206"></a><tt class="py-lineno">206</tt> <a class="py-toggle" href="#" id="__BayesC.__init__-toggle" onclick="return toggle('__BayesC.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables.__BayesC-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">priortype</tt><tt class="py-op">,</tt> <tt class="py-param">pars</tt><tt class="py-op">,</tt> <tt class="py-param">range</tt><tt class="py-op">,</tt> <tt class="py-param">resolution</tt><tt class="py-op">=</tt><tt class="py-number">512</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="__BayesC.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="__BayesC.__init__-expanded"><a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">        <tt id="link-42" class="py-name" targets="Class trunk.BIP.Bayes.general.bvariables._BayesVar=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar" class="py-name" href="#" onclick="return doclink('link-42', '_BayesVar', 'link-42');">_BayesVar</a></tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Method trunk.BIP.Bayes.Melding.FitModel.__init__()=trunk.BIP.Bayes.Melding.FitModel-class.html#__init__,Method trunk.BIP.Bayes.Melding.Meld.__init__()=trunk.BIP.Bayes.Melding.Meld-class.html#__init__,Method trunk.BIP.Bayes.Samplers.MCMC.Dream.__init__()=trunk.BIP.Bayes.Samplers.MCMC.Dream-class.html#__init__,Method trunk.BIP.Bayes.Samplers.MCMC.Metropolis.__init__()=trunk.BIP.Bayes.Samplers.MCMC.Metropolis-class.html#__init__,Method trunk.BIP.Bayes.Samplers.MCMC._Sampler.__init__()=trunk.BIP.Bayes.Samplers.MCMC._Sampler-class.html#__init__,Method trunk.BIP.Bayes.general.bvariables._BayesVar.__init__()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#__init__,Method trunk.BIP.Bayes.general.bvariables.__BayesC.__init__()=trunk.BIP.Bayes.general.bvariables.__BayesC-class.html#__init__,Method trunk.BIP.Bayes.general.bvariables.__BayesD.__init__()=trunk.BIP.Bayes.general.bvariables.__BayesD-class.html#__init__,Method trunk.BIP.SDE.gillespie.Model.__init__()=trunk.BIP.SDE.gillespie.Model-class.html#__init__,Method trunk.BIP.SMC.condensation.Condensation.__init__()=trunk.BIP.SMC.condensation.Condensation-class.html#__init__,Method trunk.BIP.SMC.condensation.GlobalData.__init__()=trunk.BIP.SMC.condensation.GlobalData-class.html#__init__,Method trunk.BIP.SMC.condensation.IterationData.__init__()=trunk.BIP.SMC.condensation.IterationData-class.html#__init__,Method trunk.BIP.SMC.condensation.Model.__init__()=trunk.BIP.SMC.condensation.Model-class.html#__init__,Method trunk.BIP.Viz.ascii.Histogram.__init__()=trunk.BIP.Viz.ascii.Histogram-class.html#__init__,Method trunk.BIP.Viz.asciihist.Histogram.__init__()=trunk.BIP.Viz.asciihist.Histogram-class.html#__init__,Method trunk.BIP.Viz.realtime.RTplot.__init__()=trunk.BIP.Viz.realtime.RTplot-class.html#__init__,Method trunk.BIP.Viz.realtime.RTpyplot.__init__()=trunk.BIP.Viz.realtime.RTpyplot-class.html#__init__"><a title="trunk.BIP.Bayes.Melding.FitModel.__init__
trunk.BIP.Bayes.Melding.Meld.__init__
trunk.BIP.Bayes.Samplers.MCMC.Dream.__init__
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.__init__
trunk.BIP.Bayes.Samplers.MCMC._Sampler.__init__
trunk.BIP.Bayes.general.bvariables._BayesVar.__init__
trunk.BIP.Bayes.general.bvariables.__BayesC.__init__
trunk.BIP.Bayes.general.bvariables.__BayesD.__init__
trunk.BIP.SDE.gillespie.Model.__init__
trunk.BIP.SMC.condensation.Condensation.__init__
trunk.BIP.SMC.condensation.GlobalData.__init__
trunk.BIP.SMC.condensation.IterationData.__init__
trunk.BIP.SMC.condensation.Model.__init__
trunk.BIP.Viz.ascii.Histogram.__init__
trunk.BIP.Viz.asciihist.Histogram.__init__
trunk.BIP.Viz.realtime.RTplot.__init__
trunk.BIP.Viz.realtime.RTpyplot.__init__" class="py-name" href="#" onclick="return doclink('link-43', '__init__', 'link-43');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">priortype</tt><tt class="py-op">,</tt> <tt class="py-name">pars</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">,</tt> <tt class="py-name">resolution</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line"> </tt>
<a name="__BayesD"></a><div id="__BayesD-def"><a name="L209"></a><tt class="py-lineno">209</tt> <a class="py-toggle" href="#" id="__BayesD-toggle" onclick="return toggle('__BayesD');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables.__BayesD-class.html">__BayesD</a><tt class="py-op">(</tt><tt class="py-base-class">_BayesVar</tt><tt class="py-op">,</tt> <tt class="py-base-class">stats</tt><tt class="py-op">.</tt><tt class="py-base-class">rv_discrete</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="__BayesD-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="__BayesD-expanded"><a name="__BayesD.__init__"></a><div id="__BayesD.__init__-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="__BayesD.__init__-toggle" onclick="return toggle('__BayesD.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="trunk.BIP.Bayes.general.bvariables.__BayesD-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">priortype</tt><tt class="py-op">,</tt> <tt class="py-param">pars</tt><tt class="py-op">,</tt> <tt class="py-param">range</tt><tt class="py-op">,</tt> <tt class="py-param">resolution</tt><tt class="py-op">=</tt><tt class="py-number">512</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="__BayesD.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="__BayesD.__init__-expanded"><a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">        <tt id="link-44" class="py-name"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar" class="py-name" href="#" onclick="return doclink('link-44', '_BayesVar', 'link-42');">_BayesVar</a></tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="trunk.BIP.Bayes.Melding.FitModel.__init__
trunk.BIP.Bayes.Melding.Meld.__init__
trunk.BIP.Bayes.Samplers.MCMC.Dream.__init__
trunk.BIP.Bayes.Samplers.MCMC.Metropolis.__init__
trunk.BIP.Bayes.Samplers.MCMC._Sampler.__init__
trunk.BIP.Bayes.general.bvariables._BayesVar.__init__
trunk.BIP.Bayes.general.bvariables.__BayesC.__init__
trunk.BIP.Bayes.general.bvariables.__BayesD.__init__
trunk.BIP.SDE.gillespie.Model.__init__
trunk.BIP.SMC.condensation.Condensation.__init__
trunk.BIP.SMC.condensation.GlobalData.__init__
trunk.BIP.SMC.condensation.IterationData.__init__
trunk.BIP.SMC.condensation.Model.__init__
trunk.BIP.Viz.ascii.Histogram.__init__
trunk.BIP.Viz.asciihist.Histogram.__init__
trunk.BIP.Viz.realtime.RTplot.__init__
trunk.BIP.Viz.realtime.RTpyplot.__init__" class="py-name" href="#" onclick="return doclink('link-45', '__init__', 'link-43');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">priortype</tt><tt class="py-op">,</tt> <tt class="py-name">pars</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">,</tt> <tt class="py-name">resolution</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">"__main__"</tt><tt class="py-op">:</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">    <tt class="py-comment">#bv = BayesVar(stats.norm,(3,1),range=(0,5))</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">    <tt class="py-name">bv</tt> <tt class="py-op">=</tt> <tt id="link-46" class="py-name" targets="Function trunk.BIP.Bayes.general.bvariables.BayesVar()=trunk.BIP.Bayes.general.bvariables-module.html#BayesVar"><a title="trunk.BIP.Bayes.general.bvariables.BayesVar" class="py-name" href="#" onclick="return doclink('link-46', 'BayesVar', 'link-46');">BayesVar</a></tt><tt class="py-op">(</tt><tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">norm</tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">range</tt><tt class="py-op">=</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">resolution</tt><tt class="py-op">=</tt><tt class="py-number">1000</tt><tt class="py-op">)</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">    <tt class="py-name">data</tt> <tt class="py-op">=</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">rvs</tt><tt class="py-op">(</tt><tt class="py-number">500</tt><tt class="py-op">)</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">    <tt class="py-name">bv</tt><tt class="py-op">.</tt><tt id="link-47" class="py-name" targets="Method trunk.BIP.Bayes.general.bvariables._BayesVar.add_data()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#add_data"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar.add_data" class="py-name" href="#" onclick="return doclink('link-47', 'add_data', 'link-47');">add_data</a></tt><tt class="py-op">(</tt><tt class="py-name">data</tt><tt class="py-op">,</tt> <tt class="py-name">stats</tt><tt class="py-op">.</tt><tt class="py-name">uniform</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">bv</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">    <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-name">bv</tt><tt class="py-op">.</tt><tt id="link-48" class="py-name"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar.get_posterior_sample" class="py-name" href="#" onclick="return doclink('link-48', 'get_posterior_sample', 'link-12');">get_posterior_sample</a></tt><tt class="py-op">(</tt><tt class="py-number">200000</tt><tt class="py-op">)</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">bv</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">bv</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">bv</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">bv</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">bv</tt><tt class="py-op">.</tt><tt class="py-name">likelihood</tt> <tt class="py-op">/</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">bv</tt><tt class="py-op">.</tt><tt class="py-name">likelihood</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'ro'</tt><tt class="py-op">,</tt> <tt class="py-name">lw</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">plot</tt><tt class="py-op">(</tt><tt class="py-name">arange</tt><tt class="py-op">(</tt><tt class="py-name">bv</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">bv</tt><tt class="py-op">.</tt><tt class="py-name">rang</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-name">bv</tt><tt class="py-op">.</tt><tt class="py-name">res</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">bv</tt><tt class="py-op">.</tt><tt id="link-49" class="py-name" targets="Method trunk.BIP.Bayes.general.bvariables._BayesVar.get_prior_dist()=trunk.BIP.Bayes.general.bvariables._BayesVar-class.html#get_prior_dist"><a title="trunk.BIP.Bayes.general.bvariables._BayesVar.get_prior_dist" class="py-name" href="#" onclick="return doclink('link-49', 'get_prior_dist', 'link-49');">get_prior_dist</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">'g+'</tt><tt class="py-op">,</tt> <tt class="py-name">lw</tt><tt class="py-op">=</tt><tt class="py-number">2</tt><tt class="py-op">)</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">    <tt class="py-keyword">print</tt> <tt class="py-name">p</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">hist</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-name">normed</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">legend</tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-string">'Likelihood'</tt><tt class="py-op">,</tt> <tt class="py-string">'Prior'</tt><tt class="py-op">,</tt> <tt class="py-string">'Posterior'</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">title</tt><tt class="py-op">(</tt><tt class="py-string">'Bayesian inference'</tt><tt class="py-op">)</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">savefig</tt><tt class="py-op">(</tt><tt class="py-string">'bayesvar.png'</tt><tt class="py-op">,</tt> <tt class="py-name">dpi</tt><tt class="py-op">=</tt><tt class="py-number">400</tt><tt class="py-op">)</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">    <tt class="py-name">P</tt><tt class="py-op">.</tt><tt class="py-name">show</tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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